This presages a baning of the Brotherhood from politics.
Egypt's army-backed government detained the Muslim Brotherhood's leader on Tuesday after a bloody crackdown on his supporters, underscoring its intention to crush the movement that had propelled the country's first freely elected president to power.
Egypt is enduring its bloodiest week of internal strife since the monarchy was overthrown in 1952, with about 900 people killed, including 100 police and soldiers, after the authorities broke up Brotherhood protest camps in Cairo last Wednesday.
A spokesman for a pro-Brotherhood alliance said the death toll among supporters of ousted Islamist president Mohamed Mursi, deposed by the military on July 3, was at about 1,400.
The turmoil has alarmed the United States and the European Union, but Israel and some Gulf Arab states led by Saudi Arabia have urged the West not to punish Cairo's new rulers.
Mohamed Badie, 70, the Brotherhood's general guide, was taken from an apartment in Nasr City in northeast Cairo, the area where protesters demanding Mursi's reinstatement had staged a vigil for six weeks before they were violently dispersed.
He was charged in July with incitement to murder during protests before Mursi's overthrow and is due to stand trial on August 25 together with his two deputies.
Footage circulated on local media showed the bearded Brotherhood leader sitting grim-faced on a sofa in a grey robe, hands folded in his lap, while a man with a rifle stands by.
The release of the images seemed designed to humiliate the Brotherhood's most senior chief, whose arrest means the top echelon of the Islamist movement is now behind bars.
After decades as an outlawed movement, the Brotherhood emerged as the best-drilled political force after Hosni Mubarak's fall in pro-democracy protests in 2011.
Now the state accuses it of al Qaeda-style militancy and subversion, charges it vehemently denies.
When the group was banned in the 1950's, they were able to establish a secret network of cells that organized Egyptian society so that when their moment came in 2011, they won the election handily.
Banning them makes sense in the short term. But its not like these guys represent a small minority of Egyptians. Eventually, the government is going to have to deal with them or the Brotherhood will undermine society from the inside.
In the meantime, the arrests will continue and the movement will be crushed.